Characterizing the genetic basis of methylome diversity in histologically normal human lung tissue

The genetic regulation of the human epigenome is not fully appreciated. Here we describe the effects of genetic variants on the DNA methylome in human lung based on methylation-quantitative trait loci (meQTL) analyses. We report 34,304 cis - and 585 trans -meQTLs, a genetic–epigenetic interaction of...

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Published inNature communications Vol. 5; no. 1; p. 3365
Main Authors Shi, Jianxin, Marconett, Crystal N., Duan, Jubao, Hyland, Paula L., Li, Peng, Wang, Zhaoming, Wheeler, William, Zhou, Beiyun, Campan, Mihaela, Lee, Diane S., Huang, Jing, Zhou, Weiyin, Triche, Tim, Amundadottir, Laufey, Warner, Andrew, Hutchinson, Amy, Chen, Po-Han, Chung, Brian S. I., Pesatori, Angela C., Consonni, Dario, Bertazzi, Pier Alberto, Bergen, Andrew W., Freedman, Mathew, Siegmund, Kimberly D., Berman, Benjamin P., Borok, Zea, Chatterjee, Nilanjan, Tucker, Margaret A., Caporaso, Neil E., Chanock, Stephen J., Laird-Offringa, Ite A., Landi, Maria Teresa
Format Journal Article
LanguageEnglish
Published London Nature Publishing Group UK 27.02.2014
Nature Publishing Group
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Abstract The genetic regulation of the human epigenome is not fully appreciated. Here we describe the effects of genetic variants on the DNA methylome in human lung based on methylation-quantitative trait loci (meQTL) analyses. We report 34,304 cis - and 585 trans -meQTLs, a genetic–epigenetic interaction of surprising magnitude, including a regulatory hotspot. These findings are replicated in both breast and kidney tissues and show distinct patterns: cis -meQTLs mostly localize to CpG sites outside of genes, promoters and CpG islands (CGIs), while trans -meQTLs are over-represented in promoter CGIs. meQTL SNPs are enriched in CTCF-binding sites, DNaseI hypersensitivity regions and histone marks. Importantly, four of the five established lung cancer risk loci in European ancestry are cis- meQTLs and, in aggregate, cis -meQTLs are enriched for lung cancer risk in a genome-wide analysis of 11,587 subjects. Thus, inherited genetic variation may affect lung carcinogenesis by regulating the human methylome. The effects of genetic variation on DNA methylation patterns are poorly understood. Here, Shi et al. systematically map methylation-quantitative trait loci in lung, breast and kidney tissue to reveal the impact of inherited variation on the human methylome, which also affects cancer risk.
AbstractList The genetic regulation of the human epigenome is not fully appreciated. Here we describe the effects of genetic variants on the DNA methylome in human lung based on methylation-quantitative trait loci (meQTL) analyses. We report 34,304 cis- and 585 trans-meQTLs, a genetic-epigenetic interaction of surprising magnitude, including a regulatory hotspot. These findings are replicated in both breast and kidney tissues and show distinct patterns: cis-meQTLs mostly localize to CpG sites outside of genes, promoters and CpG islands (CGIs), while trans-meQTLs are over-represented in promoter CGIs. meQTL SNPs are enriched in CTCF-binding sites, DNaseI hypersensitivity regions and histone marks. Importantly, four of the five established lung cancer risk loci in European ancestry are cis-meQTLs and, in aggregate, cis-meQTLs are enriched for lung cancer risk in a genome-wide analysis of 11,587 subjects. Thus, inherited genetic variation may affect lung carcinogenesis by regulating the human methylome.The genetic regulation of the human epigenome is not fully appreciated. Here we describe the effects of genetic variants on the DNA methylome in human lung based on methylation-quantitative trait loci (meQTL) analyses. We report 34,304 cis- and 585 trans-meQTLs, a genetic-epigenetic interaction of surprising magnitude, including a regulatory hotspot. These findings are replicated in both breast and kidney tissues and show distinct patterns: cis-meQTLs mostly localize to CpG sites outside of genes, promoters and CpG islands (CGIs), while trans-meQTLs are over-represented in promoter CGIs. meQTL SNPs are enriched in CTCF-binding sites, DNaseI hypersensitivity regions and histone marks. Importantly, four of the five established lung cancer risk loci in European ancestry are cis-meQTLs and, in aggregate, cis-meQTLs are enriched for lung cancer risk in a genome-wide analysis of 11,587 subjects. Thus, inherited genetic variation may affect lung carcinogenesis by regulating the human methylome.
The genetic regulation of the human epigenome is not fully appreciated. Here we describe the effects of genetic variants on the DNA methylome in human lung based on methylation-quantitative trait loci (meQTL) analyses. We report 34,304 cis- and 585 trans-meQTLs, a genetic-epigenetic interaction of surprising magnitude, including a regulatory hotspot. These findings are replicated in both breast and kidney tissues and show distinct patterns: cis-meQTLs mostly localize to CpG sites outside of genes, promoters and CpG islands (CGIs), while trans-meQTLs are over-represented in promoter CGIs. meQTL SNPs are enriched in CTCF-binding sites, DNaseI hypersensitivity regions and histone marks. Importantly, four of the five established lung cancer risk loci in European ancestry are cis-meQTLs and, in aggregate, cis-meQTLs are enriched for lung cancer risk in a genome-wide analysis of 11,587 subjects. Thus, inherited genetic variation may affect lung carcinogenesis by regulating the human methylome.
The genetic regulation of the human epigenome is not fully appreciated. Here we describe the effects of genetic variants on the DNA methylome in human lung based on methylation-quantitative trait loci (meQTL) analyses. We report 34,304 cis - and 585 trans -meQTLs, a genetic-epigenetic interaction of surprising magnitude, including a regulatory hotspot. These findings are replicated in both breast and kidney tissues and show distinct patterns: cis -meQTLs mostly localize to CpG sites outside of genes, promoters, and CpG islands (CGIs), while trans -meQTLs are over-represented in promoter CGIs. meQTL SNPs are enriched in CTCF binding sites, DNaseI hypersensitivity regions and histone marks. Importantly, 4 of the 5 established lung cancer risk loci in European ancestry are cis- meQTLs and, in aggregate, cis -meQTLs are enriched for lung cancer risk in a genome-wide analysis of 11,587 subjects. Thus, inherited genetic variation may affect lung carcinogenesis by regulating the human methylome.
The genetic regulation of the human epigenome is not fully appreciated. Here we describe the effects of genetic variants on the DNA methylome in human lung based on methylation-quantitative trait loci (meQTL) analyses. We report 34,304 cis - and 585 trans -meQTLs, a genetic–epigenetic interaction of surprising magnitude, including a regulatory hotspot. These findings are replicated in both breast and kidney tissues and show distinct patterns: cis -meQTLs mostly localize to CpG sites outside of genes, promoters and CpG islands (CGIs), while trans -meQTLs are over-represented in promoter CGIs. meQTL SNPs are enriched in CTCF-binding sites, DNaseI hypersensitivity regions and histone marks. Importantly, four of the five established lung cancer risk loci in European ancestry are cis- meQTLs and, in aggregate, cis -meQTLs are enriched for lung cancer risk in a genome-wide analysis of 11,587 subjects. Thus, inherited genetic variation may affect lung carcinogenesis by regulating the human methylome. The effects of genetic variation on DNA methylation patterns are poorly understood. Here, Shi et al. systematically map methylation-quantitative trait loci in lung, breast and kidney tissue to reveal the impact of inherited variation on the human methylome, which also affects cancer risk.
ArticleNumber 3365
Author Zhou, Beiyun
Duan, Jubao
Zhou, Weiyin
Pesatori, Angela C.
Shi, Jianxin
Wheeler, William
Chen, Po-Han
Laird-Offringa, Ite A.
Hyland, Paula L.
Chanock, Stephen J.
Bertazzi, Pier Alberto
Hutchinson, Amy
Consonni, Dario
Li, Peng
Berman, Benjamin P.
Tucker, Margaret A.
Chung, Brian S. I.
Borok, Zea
Freedman, Mathew
Campan, Mihaela
Amundadottir, Laufey
Lee, Diane S.
Triche, Tim
Landi, Maria Teresa
Warner, Andrew
Siegmund, Kimberly D.
Caporaso, Neil E.
Chatterjee, Nilanjan
Huang, Jing
Marconett, Crystal N.
Wang, Zhaoming
Bergen, Andrew W.
AuthorAffiliation 8 Bioinformatics Division, Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90089, USA
7 Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, NIH, DHHS, Bethesda, MD 20892, USA
10 Unit of Epidemiology, IRCCS Fondazione Ca’ Granda Ospedale Maggiore Policlinico and Department of Clinical Sciences and Community Health, University of Milan, Milan, 20122, Italy
3 Department of Biochemistry and Molecular Biology, USC/Norris Comprehensive Cancer Center, Keck School of Medicine, Los Angeles, CA 90089, USA
9 Pathology/Histotechnology Laboratory, Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, 21702, USA
13 Department of Medical Oncology, The Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215
4 Center for Psychiatric Genetics, Department of Psychiatry and Behavioral Sciences, North Shore University Health System Research Ins
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BackLink https://www.ncbi.nlm.nih.gov/pubmed/24572595$$D View this record in MEDLINE/PubMed
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10.1038/nature09534
10.1038/nature07385
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Snippet The genetic regulation of the human epigenome is not fully appreciated. Here we describe the effects of genetic variants on the DNA methylome in human lung...
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pubmed
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SubjectTerms 631/208/2489/2487/2486
631/208/726/649
631/67/1612
Breast - metabolism
Carcinogenesis
CpG Islands - genetics
DNA Methylation
Epistasis, Genetic
Gene mapping
Genetic diversity
Genetic Predisposition to Disease - ethnology
Genetic Predisposition to Disease - genetics
Genetic variance
Genetic Variation
Genome-Wide Association Study
Genotype
Health risks
Humanities and Social Sciences
Humans
Hypersensitivity
Kidney - metabolism
Lung - metabolism
Lung cancer
Lung Neoplasms - ethnology
Lung Neoplasms - genetics
multidisciplinary
Polymorphism, Single Nucleotide
Promoter Regions, Genetic - genetics
Quantitative Trait Loci - genetics
Risk Factors
Science
Science (multidisciplinary)
White People - genetics
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Title Characterizing the genetic basis of methylome diversity in histologically normal human lung tissue
URI https://link.springer.com/article/10.1038/ncomms4365
https://www.ncbi.nlm.nih.gov/pubmed/24572595
https://www.proquest.com/docview/1502606688
https://www.proquest.com/docview/1503551301
https://pubmed.ncbi.nlm.nih.gov/PMC3982882
Volume 5
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